added pipeline commands which involved change to command factory and command class...

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index b2474c52e4ea1188c042550033f6e27581a6f4a3..3240860fc329bed3b9551359a6ff1b23a16b8019 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,43 +11,46 @@
  */
 
 #include "command.hpp"
-#include "coverage.h"
 #include "fullmatrix.h"
+#include "libshuff.h"
 
-using namespace std;
 
 class GlobalData;
 
 class LibShuffCommand : public Command {
        
-       public:
-               LibShuffCommand();      
-               ~LibShuffCommand();
-               int execute();  
+public:
+       LibShuffCommand(string);
+       LibShuffCommand();      
+       ~LibShuffCommand(){};
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
+
+private:
+       vector<string> groupNames;
        
-       private:
-               vector< vector<float> > cValues; // vector of coverage scores, one for each comparison.
-               vector<float> deltaValues; // vector of delta scores, one for each comparison.
-               vector<float> sumDelta; //sum of delta scores, one for each comparison.
-               vector<float> sumDeltaSig; //number of random  matrixes with that delta value or ??
-               vector< vector<float> > rsumDelta; //vector< vector<sumdelta scores for a given comparison> >
-               vector<string> groupComb;
-               
-               
-               void setGroups();
-               int findIndex(float, int);
-               void printCoverageFile(float);
-               void printSummaryFile();
-
-               GlobalData* globaldata;
-               Coverage* coverage;
-               FullMatrix* matrix;
-               float cutOff;
-               int numGroups, numComp, iters;
-               string coverageFile, summaryFile;
-               ofstream out, outSum;
-                               
-               
+       void setGroups();
+       int printCoverageFile();
+       int printSummaryFile();
+
+       GlobalData* globaldata;
+       FullMatrix* matrix;
+       Libshuff* form;
+       float cutOff, step;
+       int numGroups, numComp, iters;
+       string coverageFile, summaryFile;
+       vector<vector<int> > pValueCounts;
+       vector<vector<double> > savedDXYValues;
+       vector<vector<vector<double> > > savedMinValues;
+
+       bool abort;
+       string outputFile, groups, userform, savegroups, outputDir;
+       vector<string> Groups, outputNames; //holds groups to be used
+       map<string, vector<string> > outputTypes;
 };
 
 #endif